Stopping boats may well have stopped mass drownings, but is Australia endangering the people it returns?

All week, Scott Morrison had been wishing away the little boat from India. The Immigration Minister steadfastly refused to acknowledge its existence or that of its human cargo, 153 Tamil asylum seekers; or that of another boat carrying 50 Tamils, which had come from Sri Lanka. By week's end, it seemed Morrison's wish had come true.

In a high-stakes, high seas operation – which Morrison never confirmed, preferring to call it speculation – Australia set out to deliver these boat people back into the hands of Sri Lanka, the regime they had fled, a country the United Nations suspects of systematic abductions, torture, rape, extrajudicial killings and the "disappearing" of its citizens. Now Australia had "disappeared" their boats. It was as if their odyssey had never happened.

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They seemed real enough last Saturday, when Fairfax Media and other news organisations reached a satellite phone on the first vessel, a 25-metre fishing trawler, and spoke to its passengers.

"The wind is increasing and there are huge waves," said a Tamil who called himself Duke. "We are all at threat."

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They reported they were 175 nautical miles west of Christmas Island, having left Puducherry in southern India 15 days earlier, on June 13. The boat's phone was cut off that day.

Even as Morrison and Prime Minister Tony Abbott held fast to their policy of never discussing "on-water matters", they seized the opportunity to remind Australians that they had stopped the boats. Not a single asylum boat had landed in Australia for six months.

These two boats, though, would have been different. They had not taken the usual route, via Indonesia.

By Wednesday, it emerged that the Australian navy had boarded both vessels and transferred their passengers to Customs boats. The Tamils from the second boat at least, near the Cocos Islands, and likely all of them, were subjected to "screening" that amounted to four questions – name, country of origin, place of disembarkation and why they had left – which was a big cull from the usual 19 questions.

Then, it appears, Customs shipped them towards an undisclosed rendezvous point in international waters to be transferred to the Sri Lankan navy. Sri Lanka's officials both confirmed and denied the planned transfer. The UN refugee agency expressed "profound concern".

"Australia's moral, ethical and legal compass has been lost at sea," said Trevor Grant, from Australia's Tamil Refugee Council.

The council said at least 11 people on the fishing trawler had been jailed and tortured in Sri Lanka, according to a relative of several of the passengers.

But the swift operation fulfilled Morrison's pledge last September, when he declared that "people who may seek to come from Sri Lanka would be intercepted outside of our sea border and returned directly – and all of them"; and again in October, when he said "anyone who may have come from Sri Lanka should know that they will go back to Sri Lanka. We have an arrangement with the Sri Lankan government and … and, preferably, they will all go back."

The Abbott government has singled out Sri Lankans for special treatment, or mistreatment, if the conclusions of successive international reports on the country's human rights abuses are accepted. Australia subjects only Sri Lankans to "enhanced", or expedited, screening. Australia's "arrangement" with Sri Lanka is all about stopping the boats carrying its nationals.

The Tamil boat exodus to Australia did not happen during Sri Lanka’s 26-year civil war, in which atrocities on both sides – the Sinhalese majority and the Liberation Tigers of Tamil Eelam – were well documented. Rather, the flood of boats erupted almost three years after the official end to the war in 2009. Between January 2012 and late last year, Australia received more than 8300 Sri Lankans by boat.

Why? Other destination countries are asking the same question. In the foreword to a 2014 report that documents the testimony of 40 Tamils who fled to Britain, South Africa's Archbishop Desmond Tutu writes: "It shows how anyone remotely connected with the losing side in the civil war is being hunted down, tortured and raped, five years after the guns fell silent. Shockingly, more than half of the abductions in the report took place as recently as 2013-14 ... The sheer viciousness and brutality of the sexual violence is staggering ... Thirty-five of the witnesses were forced to sign confessions in Sinhala, a language they do not understand."

Even at the height of the influx of Sri Lankan boat people to Australia last year, the Department of Immigration and Border Protection reported that 52 per cent of these asylum seekers were granted protection visas. Traditionally, 90 per cent were found to be genuine refugees, says Emily Howie, director of advocacy and research at the Human Rights Law Centre. And yet the government now wants "all" returned.

While Abbott said this week that Sri Lanka was not "everyone's idea of the ideal society", he claimed it was a country "at peace". His analysis contradicted the Department of Foreign Affairs and Trade, which continues to warn Australians to exercise a "high degree of caution" due to the unpredictable security environment. Still, on the question of sending Sri Lankans home, Abbott was "absolutely confident that no harm would come to anyone who has been in our charge".

"That is an utterly erroneous presumption," says Ben Saul, professor of international law at the University of Sydney. Saul warns that Australia is at grave risk of being found guilty under international law of refoulement – returning people to a country where their life or freedom would be threatened because of their race, religion, nationality, political opinions or membership of a social group.

When Sri Lanka hosted the Commonwealth Heads of Government Meeting last November, Canada's conservative Prime Minister, Stephen Harper, boycotted the event to protest against Sri Lanka's failure to investigate its troops over alleged war crimes and the slaughter of as many as 40,000 civilians in the final stages of the civil war. Britain’s Prime Minister David Cameron attended but spoke out on human rights. Abbott went bearing a gift of two patrol boats, worth $2 million, so Sri Lanka could help to stop the "curse" of people smuggling.

Abbott said that while his government "deplores the use of torture, we accept that sometimes in difficult circumstances difficult things happen".

Sri Lanka is refusing to co-operate with a UN investigation into its alleged war crimes, arguing it is being treated in an "unforgiving manner" for defeating a ruthless terrorist group in the Tamil Tigers. Australia chose not to co-sponsor the investigation push.

Of course, no boat arrivals – from Sri Lanka or anywhere else – have had any prospect gaining asylum in Australia since then Labor prime minister Kevin Rudd shut that door last July. But some passengers on board the latest Tamil boats thought they were bound for New Zealand. They were acutely aware they would be sent to Manus Island or Nauru if they reached Australia.

"I thought maybe it was to Italy, or France, or Tunisia," said Ragajini, the 32-year-old wife of one of the men on the fishing trawler. "I did not know where he was going and he did not know, either."

Ragajini, who has their two children with her, sobbed as she spoke from the Aliyar camp for Tamil refugees in the Coimbatore district in the far west of the Indian state of Tamil Nadu. Her husband had crippling debts and had needed to escape to a country where he could earn money, she said.

Australia – under Labor and Coalition governments – has forced more than 1100 asylum seekers to return to Sri Lanka since October 2012. Sureh, a 35-year-old Tamil on a bridging visa in Melbourne, says he fears Australia will soon send him back to certain torture. A former aid worker who cared for displaced people in northern Sri Lanka, he was arrested and accused of being a Tamil Tiger.

"I was not subject to extreme torture like my friends," he says. "They would take us into a room. They tortured us there. They asked my friend to remove his clothes. They inserted an S-Lon [PVC] pipe through his anus. He was screaming."

Emily Howie spent more than five months in Sri Lanka while preparing a report published in March, Can't Flee, Can't Stay – Australia's Interception and Return of Sri Lankan Asylum Seekers. She interviewed people who alleged they were beaten or witnessed assaults after the Sri Lankan navy intercepted their boats. She believes Australia, by helping to stop their escape, is denying their human right to free movement and risks being accused of "aiding and assisting" in their torture and mistreatment.

Australia claims there is no evidence of mistreatment of its returnees. But Howie's report describes how the Australian Federal Police, with a base in Colombo, failed to investigate a complaint of "severe torture" against Sri Lanka's police. Howie obtained a cable, under freedom-of-information laws, that revealed the Sri Lankans denied the claim but invited the AFP to visit the alleged victim in custody. The AFP had reported: "In the interests of keeping our distance from the Sri Lankan investigations, we do not intend to take up the offer to meet with him." Rather, it had "sighted the suspect, who appears in good health".

"This incident reveals a wilful blindness to the ongoing real risk of ill-treatment or harm of returnees at the hands of Australia's Sri Lankan partners," Howie wrote.

The expectation of a forced return led to the death of 29-year-old Leo Seemanpillai, who set himself ablaze in Geelong in May, Grant says. Another Tamil asylum seeker on a bridging visa attempted self-immolation in Melbourne last month but was saved by his flatmates. Grant says the 40-year-old man had been tortured in 2007 for providing food to the Tamil Tigers. He recently learnt that his brother had been "disappeared" within Sri Lanka's prison system.

Morrison, defending the secrecy around the operation this week, said: "Public curiosity is not the same as the public interest ... and what is in the national interest is that we maintain the integrity of an operation that is saving lives at sea and protecting the integrity of our borders."

Stopping boats may well have stopped mass drownings, but is Australia endangering the people it returns? In a June 25 statement, the Asian Human Rights Commission reported "a pandemic of abuse by state agents" in Sri Lanka. It published a book last year on 400 cases of torture, taken from about 1500 cases it had studied. Common methods of torture ranged from "beatings, sometimes with the victim hung upside down, to the use of chili powder applied to the eyes and genitals".

The relative of the of the people on the Australia-bound fishing trawler described his own torture, in 2006, to Aran Mylvaganam, convenor with the Tamil Refugee Council. “He told me he was bashed with a plastic pipe filled with sand. Rope was tied to his thumbs and he was hung from a ceiling. These sessions would last for six hours and happened regularly. They had been demanding he admit to being a Tamil Tiger, but he wasn’t.”

Given that 57 of the people from the fishing trawler had already fled from Sri Lanka to India, Ben Saul says Australia should, at the very least, send them back to India, not to the country of their alleged persecution.

‘‘Sri Lanka has become a virtual one-party state run by a dynastic family, the Rajapaksas,’’ Saul says. ‘‘They’ve destroyed the rule of law by dismissing the chief justice; there are still thousands of Tamil Tigers detained without charge. There are attacks on the independent media, including the killings of journalists. You certainly can’t say Sri Lanka is a rehabilitated state on the path to democracy ... but our government seems to have bought the official line from Sri Lanka.”

Abbott told radio 3AW on Thursday: "It is a peaceful country. I don't say it's a perfect country. Not even Australia is that."